Professor Samantha Sampson

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1 Career and Employment History Professor Samantha Sampson 2013-present Associate Professor, NRF SARChI Chair in Mycobactomics DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa Mycobactomics (integrating data-rich methodologies through use of computational approaches) Wellcome Trust Research Career Development Fellow, Research Associate Section of Microbiology/Centre for Molecular Microbiology and Infection Imperial College London, London, UK TB host-pathogen interactions Visiting Scientist Harvard School of Public Health, Boston, USA Development of a novel pulmonary delivery method for TB vaccines Post-doctoral Research Fellow Harvard School of Public Health, Boston, USA Safety and efficacy studies of a live attenuated auxotrophic TB vaccine candidate Ph.D. Project student GlaxoSmithKline, Stevenage, UK Cloning, expression and characterization of a cell-wall associated PPE protein Ph.D. Student University of Stellenbosch, Cape Town, South Africa Characterization of genetic diversity of clinical isolates of Mycobacterium tuberculosis Academic Qualifications University of Stellenbosch, Cape Town, South Africa 2002 Ph.D. Thesis title: Mycobacterium tuberculosis: Genetic and Phenotypic Comparison 1997 M.Sc. (Medical Biochemistry), graduated cum laude (equivalent to 1 st class) Thesis title: Characterization of mechanisms leading to Mycobacterium tuberculosis strain diversity 1995 B.Sc. Hons. (Medical Biochemistry), graduated cum laude (equivalent to 1 st class) 1994 B.Sc. (Chemistry and Biochemistry) Funding (selected grants, awarded in open competition) 2013-present South African Research Chair Initiative (SARChI) award; ZAR7,500,000 (PI) NRF Competitive Support for Unrated Researchers award; ZAR1,015,000 (PI) NRF-South Africa/Tunisia Research Cooperation Programme; ZAR935,500 (co-pi) 2015 Royal Society (UK)/ Newton Fund International Exchanges Scheme; 3,000 (PI) 2014 Harry and Doris Crossley Foundation Project funding, ZAR10,950 and ZAR9,900 (PI) Wellcome Trust Research Career Development Fellowship; 490,000 (PI) Royal Society Research Grant; 10,000 (PI) Bill and Melinda Gates Foundation Grand Challenges Explorations Grant; US$100,000 (PI) Prof. Samantha Sampson, CV Page 1 of 6

2 Citation Report Source: Total citations: Average citations per year ( ): Average citations per article: i10-index: H-index: Google Scholar (last accessed March 2016) Publications journal articles Newton-Foot M, Warren RM, Sampson SL, van Helden PD, Gey van Pittius NC. The plasmid-mediated evolution of the mycobacterial ESX (Type VII) secretion systems. BMC Evol Biol (1):62 Impact Factor: Phelan JE, Coll F, Bergval I, Anthony RM, Warren RM, Sampson SL and 24 other authors. Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics (2016). 17:151 Impact Factor: 3.99 Sampson SL. Strength in Diversity: Hidden Genetic Depths of Mycobacterium tuberculosis. Invited Spotlight article, Trends in Microbiology (2):82-84 Impact Factor: Black P, De Vos M, Louw G, Van der Merwe R, Dippenaar A, Streicher E, Abdallah A, Sampson S, Victor T, Dolby T, Simpson J, Van Helden P, Warren R, Pain A. Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. BMC Genomics (1):857 Impact Factor: 3.99 Dippenaar A, Parsons SDC, Sampson SL, Van der Merwe RG, Drewe JA, Abdallah AM, Siame KK, Gey van Pittius NC, Van Helden PD, Pain A, Warren RM. Whole genome sequence analysis of Mycobacterium suricattae. Tuberculosis (6):682-8 Impact Factor: Pule C, Sampson SL (corresponding author), Warren RM, Black P, Van Helden PD, Victor TC, Louw GE. Efflux pump inhibitors: targeting mycobacterial efflux systems to enhance TB therapy. Journal of Antimicrobial Chemotherapy (1): Impact Factor: Streicher EM, Sampson SL, Dheda K, Dolby T, Simpson J, Victor TC, Gey van Pittius NC, van Helden PD, Warren RM. Molecular epidemiological interpretation of the extensively drug resistant tuberculosis epidemic in South Africa J Clin Microbiol (11): Impact Factor: Whitfield MG, Warren RM, Streicher EM, Sampson SL, Sirgel F, Van Helden PD, Mercante A, Willby M, Hughes K, Birkness K, Morlock G, Van Rie A, Posey J. Mycobacterium tuberculosis pnca polymorphisms that do not confer pyrazinamide resistance at a breakpoint concentration of 100 µg/ml in MGIT. J Clin Microbiol (11): Impact Factor: Whitfield MG, Soeters HM, Warren RM, York T, Sampson SL, Streicher EM, van Helden PD, van Rie A. A Global Perspective on Pyrazinamide Resistance: Systematic Review and Meta-analysis. PLOS ONE (7):e Impact Factor: Fishbein S, Van Wyk N, Warren RM, Sampson SL. Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity. Molecular Microbiology doi: /mmi. Impact Factor: Fortuin S, Tomazella G, Nagayaryan N, Sampson S, Gey van Pittius N, Soares N, Wiker H, De Souza G, Warren R. Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: Expanding the mycobacterial phosphoproteome catalogue. Frontiers in Microbiology, section Microbial Physiology and Metabolism doi: /fmicb Impact Factor: Fang Z, Sampson SL, Warren RM, Gey van Pittius NC, Newton-Foot M. Iron acquisition Strategies in Mycobacteria. Tuberculosis (2): Impact Factor: Van der Merwe RG, Van Helden PD, Warren RM, Sampson SL, Gey van Pittius NC. Phage-based detection of bacterial pathogens. Analyst DOI: /C4AN00208C Impact Factor: Sampson SL, Saraiva, L, Gustafsson K, Jayasinghe SN, Robertson BD. Cell electrospinning an in vitro and in vivo study. Small (1):78-82, smll Impact Factor: Andreu N, Zelmer A, Sampson SL, Ikeh M, Bancroft GJ, Schaible UE, Robertson BD, Wiles S. Rapid in vivo assessment of drug efficacy against Mycobacterium tuberculosis using an improved firefly luciferase. Journal of Antimicrobial Chemotherapy (9): Impact Factor: Prof. Samantha Sampson, CV Page 2 of 6

3 Publications - journal articles (continued) Vordermeier HM, Hewinson RG, Wilkinson RJ, Wilkinson KA, Gideon HP, Young DB, Sampson SL. Conserved Immune Recognition Hierarchy of Mycobacterial PE/PPE Proteins During Infection in Natural Hosts. PLoS ONE (8): e Impact Factor: Sampson SL, Mansfield KG, Carville A, Magee DM, Quitugua TN, Howerth EW, Bloom BR, Hondalus MK. Extended safety and efficacy studies of a live attenuated double leucine and pantothenate auxotroph of Mycobacterium tuberculosis as a vaccine candidate. Vaccine (29-30): Impact Factor: Goldstone RM, Goonesekera SD, Bloom BR, Sampson SL. The transcriptional regulator Rv0485 modulates the expression of a pe/ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun (10): Impact Factor: Wong YL, Sampson SL, Germishuizen WA, Goonesekera S, Caponetti G, Sadoff J, Bloom BR, Edwards D. Drying a tuberculosis vaccine without freezing. PNAS (8): Impact Factor: Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol Biol (1):95 Impact Factor: Sampson SL, Dascher CC, Sambandamurthy VK, Russell RG, Jacobs WR Jr., Bloom BR, Hondalus MK. Protection elicited by a double leucine and pantothenate auxotroph of Mycobacterium tuberculosis in guinea pigs. Infect Immun (5): Impact Factor: Sampson SL, Richardson M, Van Helden, PD, Warren RM. IS6110-mediated deletion polymorphism in isogenic strains of Mycobacterium tuberculosis. J Clin Microbiol (2):895-8 Impact Factor: Richardson M, Van der Spuy GD, Sampson SL, Beyers N, Van Helden PD, Warren RM. Stability of Polymorphic GC- Rich Repeat Sequence-Containing Regions of Mycobacterium tuberculosis. J Clin Microbiol (3): Impact Factor: Gey van Pittius NC, Sampson SL, Warren RM, van Helden PD. Genome variation in Mycobacterium tuberculosis. South African Journal of Science Sampson SL, Rengarajan J, Rubin, EJ. Bacterial genomics and vaccine design. Expert Review of Vaccines (3): Impact Factor: Sampson SL, Warren RM, Richardson M, Victor TC, Jordaan AM, Van Der Spuy GD, Van Helden PD. IS6110-mediated deletion polymorphism in the DR region of clinical isolates of Mycobacterium tuberculosis. J Bacteriol (9): Warren RM, Streicher EM, Sampson SL, Van Der Spuy GD, Richardson M, Nguyen D, Behr MA, Victor TC, Van Helden PD. Microevolution of the Direct Repeat Region of Mycobacterium tuberculosis: Implications for Interpretation of Spoligotyping Data. J Clin Microbiol (12): Sampson SL, Lukey P, Warren RM, van Helden PD, Richardson M, Everett MJ. Expression, characterization and subcellular localization of the Mycobacterium tuberculosis PPE gene Rv1917c. Tuberculosis (5-6): Sampson S, Warren R, Richardson M, van der Spuy G, van Helden P. IS6110 insertions in Mycobacterium tuberculosis: predominantly into coding regions. J Clin Microbiol (9): Upton AM, Mushtaq A, Victor TC, Sampson SL, Sandy J, Smith DM, van Helden PD, Sim E. Arylamine N- acetyltransferase of Mycobacterium tuberculosis is a polymorphic enzyme and a site of isoniazid metabolism. Mol Microbiol (2): Warren RM, Richardson M, Sampson SL, van der Spuy GD, Bourn W, Hauman JH, Heersma H, Hide W, Beyers N, van Helden PD. Molecular evolution of Mycobacterium tuberculosis: phylogenetic reconstruction of clonal expansion. Tuberculosis (4): Warren RM, Sampson SL, Richardson M, Van Der Spuy GD, Lombard CJ, Victor TC, van Helden PD. Mapping of IS6110 flanking regions in clinical isolates of Mycobacterium tuberculosis demonstrates genome plasticity. Mol Microbiol (6): Sampson SL, Warren RM, Richardson M, van der Spuy GD, van Helden PD. Disruption of coding regions by IS6110 insertion in Mycobacterium tuberculosis. Tuber Lung Dis (6): Van Rie A, Warren RM, Beyers N, Gie RP, Classen CN, Richardson M, Sampson SL, Victor TC, van Helden PD. Transmission of a multidrug-resistant Mycobacterium tuberculosis strain resembling "strain W" among noninstitutionalized, human immunodeficiency virus-seronegative patients. J Infect Dis (5): Prof. Samantha Sampson, CV Page 3 of 6

4 Publications - journal articles (continued) Warren R, Richardson M, Van der Spuy G, Victor T, Sampson S, Beyers N, van Helden P. DNA fingerprinting and molecular epidemiology of TB: use and interpretation in an epidemic setting. Electrophoresis (8): Warren R, Richardson M, Sampson S, Hauman JH, Beyers N, Donald PR, van Helden PD. Genotyping of Mycobacterium tuberculosis with Additional Markers Enhances Accuracy in Epidemiological Studies. J Clin Microbiol : Publications book chapters Loxton AG, Hondalus MK, Sampson SL. TB vaccine assessment. Book chapter in: Delivery Systems for Tuberculosis Prevention and Treatment; Wiley. Editors: Anthony J. Hickey, Amit Misra, P. Bernard Fourie. In press Vordermeier M, Jones GJ, Sampson SL, Gordon SV. Post-genomic antigen discovery: bioinformatical approaches to reveal novel T-cell antigens of Mycobacterium bovis. Book chapter in: Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines; Springer. Editors: Dr Darren Flower and Prof Yvonne Perrie, ISBN Immunomics Reviews, Volume 5, 2013, pp Scientific Presentations Devastating Diseases and a Sustainable Society: Learning from the Tubercle Bacillus. Science for Sustainability conference, Amsterdam, The Netherlands, November 2015, Keynote Presentation Whole genome sequence interrogation of drug resistant Mycobacterium tuberculosis. The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project seminar series, Durban, March 2015, Invited seminar In vivo imaging of Mycobacterium tuberculosis infection. UK-SA Seminar on Imaging in Host-Pathogen Interactions, Cape Town, November 2014, Invited talk Mice in TB Research what s new and how is this useful in a Southern African context? Southern African Consortium for Research Excellence TB workshop Understanding and Intervening in tuberculosis in Southern Africa. August 2013, Invited seminar. TB Host-pathogen interactions. Antibodies and Immune Responses Subject Day. Prince s Teaching Institute, UK. January 2012, Invited Lecture Patent United States Patent Number: US 7,758, 874 B2; Attenuated Mycobacterium tuberculosis vaccines. Jacobs WR Jr, Bloom BR, Hondalus MK, Sampson SL, Sambandamurthy V. July 2010 Publications - popular science writing What needs to be added to South Africa s anti-tb toolbox. The Conversation, 15 May 2015; Republished under Creative Commons licence by: Biznews, 16 May 2015; The Big Issue, 18 May 2015; SciBraai, 18 May 2015 Integrated approach to TB research: Key to success. Spice4life.co.za. 25 March 2014 Fresh Hope for MDR-TB patients. Sowetan. 24 March 2014 Prof. Samantha Sampson, CV Page 4 of 6

5 External Activities Invited reviewer of manuscripts for the following international journals: BBA Molecular Cell Research, Frontiers in Cellular and Infection Microbiology, Immunobiology, Immunology, International Journal of Tuberculosis and Lung Disease, Journal of Cellular Physiology, Molecular Microbiology, Microbiology, PLoS One, PNAS, Tuberculosis Invited reviewer of funding applications for: Royal Society (UK), South African National Research Foundation, Portuguese Foundation for Science and Technology, Netherlands Organisation for Scientific Research, Research Council of Norway Professional Memberships: Association of South African Women in Science and Engineering, South African Society for Microbiology, South African Immunology Society, South African Society for Bioinformatics Teaching Activities Student supervision, Stellenbosch University: PhD (currently: 4 as primary supervisor, 4 as co-supervisor; graduated: 2 as co-supervisor) MSc (currently: 3 as primary supervisor, 3 as co-supervisor) BSc Hons (currently: 1 as primary supervisor, 1 as co-supervisor; graduated: 4 as primary supervisor) Student supervision, Imperial College London: MRes (Masters in Research) Microbial Pathogenesis project students, 2009, 2010, 2011 BSc Immunity and Infection project students, 2008, 2009, 2010, 2012 Wellcome Trust PhD rotation students, 2006, 2011 (Co-supervised) Module co-ordinator: BSc Immunity and Infection, Infection and Host responses Module, Imperial College London BSc Hons in Molecular Biology and Human Genetics, Mycobacteriology Module, Stellenbosch University Lectures, Imperial College London: New Advances in TB vaccination; BSc Global Health TB Vaccines Old And New; BSc Immunity and Infection, BSc Medical Microbiology M. tuberculosis ESX virulence locus; BSc Immunity and Infection TB Animal Models; BSc Immunity and Infection; MRes Microbial Pathogenesis M. tuberculosis ESX virulence locus; BSc Immunity and Infection TB Host-pathogen interactions, MSc Molecular Medicine Tutoring: Problem-based learning: Doctor and Patient course (Year 1), 2008 Teaching courses attended, Centre for Educational Development, Imperial College London: Supporting Teaching and Learning Programme (SLTP), February - December 2011 A Practical Introduction to Problem Based Learning (PBL), September 2007 Communicating Knowledge, September 2007 Starting teaching for postdocs Modules 1 & 2, June 2007 Issues and techniques for one-off teaching sessions, February 2007 Assisting with PhD supervision, February 2007 Prof. Samantha Sampson, CV Page 5 of 6

6 Personal Development HERS-SA Academy, a week-long professional development opportunity for the advancement and leadership development of women in the Higher Education sector, September 2015 Managing your first research group Workshop, Imperial College, April 2013 Selected participant in TANDEMplusIDEA, an EU-funded international mentoring, networking and training programme, Research Proposal Development Workshop, Imperial College, November 2009 Personal Review and Development Plan - Reviewers training workshop, Imperial College, February 2009 Effective Recruitment & Selection workshop, Imperial College, October 2006 Skills and experience summary Over 20 years experience in the TB research field. Extensive molecular, microbiological and immunological experience. Experience with 4 different TB animal models and in vitro (macrophage) infection models Have contributed to development of SOPs for category 3 containment labs, and have trained and managed students, technicians and post-doctoral researchers working in this setting. Management: Have managed day-to-day running of laboratory, research budgets and personnel. In my previous position, I trained and supervised 3 technicians, 4 undergraduate and 5 post-graduate students. I currently supervise or co-supervise 15 post-graduate students (MSc and PhD) and 3 post-doctoral fellows. Teaching: Graduate and undergraduate research project supervision, give lectures and tutorials and participate in student assessments; was responsible for the Host Responses to Infection module on Imperial College BSc Immunity and Infection course - this involved development of course content, setting and marking exams, student assessments and related administrative responsibilities. I currently co-ordinate the Mycobacteriology module of our Departmental BSc Hons course. Good Clinical Practice (GCP) Level 2 certificate Contact Details Tel: +27 (0) ssampson@sun.ac.za Skype: samantha.sampson1 website: Prof. Samantha Sampson, CV Page 6 of 6